Hi @G_Lab
It appears that the system python is being used instead of conda python. That can lead to odd problems. And not just during the initial start-up phase, but later within the application itself (core functionality issues, tool dependency problems).
Try creating a virtualenv .venv in your ../galaxy/ directory and allowing Galaxy to manage dependencies. Shut down Galaxy first, add the .venv, then rerun sh run.sh. If that doesn’t work, try again with a fresh checkout.
Simple instructions are here, for OSX, but it describes the general process that you can adapt it for your OS: Example step-by-step for a basic local Galaxy install with an admin account created
More about dependency resolvers is covered in the Galaxy Admin docs here:
- https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
- https://docs.galaxyproject.org/en/master/admin/conda_faq.html
Let us know how this goes, and we can help more if needed.
Thanks!
cc @dannon (he suggested the first-pass solution above)